Consensus tree constructed from 100 maximum likelihood trees. The branch lengths and the scale bar are proportional to nucleotide differences. Bootstrap values out of a total of 100 are given at the nodes. The sequence of Aquifex pyrophilus was used as outgroup. The OTU numbers of the Rya WWTP sequences are given with the total number of sequences within that OTU in parentheses. The cluster names are in accordance with DeLong [30] Selleckchem Epigenetics Compound Library and Jurgens [31]. Dynamics of the Archaea community The community

composition, as assessed by T-RFLP, changed little throughout the monitored period. The difference, measured as Bray-Curtis distance, between the terminal restriction fragment (TRF) profile of the first sample in the time series, May 16, 2003, and all following samples was on average only 5.8 ± 6.3% and 5.4 ± 7.1% for the AluI and RsaI analysis, respectively (Figure  6). On two occasions, in October 2003 and in January 2004, the Bray-Curtis distance peaked, indicating a deviation from the community composition FK506 mw at the beginning of the time series. The difference between the TRF profiles of May 16, 2003 and May 22, 2007,

four years later, was 10% and 0% for the AluI and RsaI analysis, respectively. However, the sensitivity of the T-RFLP analysis is limited and TRFs of low abundance cannot be detected. Thus, a Bray-Curtis distance of oxyclozanide 0% between the TRF profiles of two samples does not indicate identical community composition since there may be differences in the composition of Archaea of low abundance. To get a rough estimate of the sensitivity of the T-RFLP method, a comparison

was made between the theoretical TRF profile of the clone library and the observed TRF profile from the same sample. The comparison showed that only TRFs with a relative abundance higher than 20% in the clone library were observed in the TRF profile (Table 3). Thus, the T-RFLP analysis shows the dynamics of the major groups of Archaea in the activated sludge. The relative abundances of the observed TRFs in all TRF profiles in the time series are shown in Figures  7 and 8. Figure 6 Community stability. The stability of the archaeal community is illustrated by plotting the difference, measured as Bray-Curtis distance, between the TRF profile of the first sample in the time series, May 16, 2003, and all following samples. The Bray-Curtis distance is calculated by comparing the relative abundances of the TRFs in the TRF profiles and is low for similar profiles. Results from both the AluI and the RsaI analysis are shown. Table 3 Observed and predicted TRF lengths a Observed TRF lengths T-RFLP 2007-05-22 Predicted TRF lengths, clone library 2007-05-22 AluI %b RsaI %b AluI RsaI %c Identity         84 80 1% Thaumarchaeota/Cluster 1.